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1.
Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to the reduction of genetic diversity. Estimates of marginal contributions of ancestors suggest that the bottlenecks arose mainly because related stallions had been used for breeding. A tendency for an increase in inbreeding coefficients was observed. F‐statistics revealed that a small effective population size majorly contributed to this increase, although non‐random mating in particular regions also contributed. Because the bottlenecks are thought to have reduced the effective population size, our results imply that mitigation of bottlenecks is important for conservation. To this end, breeding should involve genetically diverse stallions. In addition, to prevent non‐random mating observed in particular regions, efforts should be made to plan mating with consideration of kinships.  相似文献   

2.
The accumulation of inbreeding and the loss of genetic diversity is a potential problem in Holstein dairy cattle. The goal of this study was to estimate inbreeding levels and other measures of genetic diversity, using pedigree information from Iranian Holstein cattle. Edited pedigree included 1 048 572 animals. The average number of discrete generation equivalents and pedigree completeness index reached 13.4 and 90%, respectively. The rate of inbreeding was 0.3% per year. Effective number of founders, founder genomes, non‐founders and ancestors of animals born between 2003 and 2011 were 503, 15.6, 16.1 and 25.7, respectively. It was proven that the unequal founder contributions as well as bottlenecks and genetic drift were important reasons for the loss of genetic diversity in the population. The top 10 ancestors with the highest marginal genetic contributions to animals born between 2003 and 2011 and with the highest contributions to inbreeding were 48.20% and 63.94%, respectively. Analyses revealed that the most important cause of genetic diversity loss was genetic drift accumulated over non‐founder generations, which occurred due to small effective population size. Therefore, it seems that managing selection and mating decisions are controlling future co‐ancestry and inbreeding, which would lead to better handling of the effective population size.  相似文献   

3.
The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32?% of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50?% of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8?% for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64?%. The average relatedness coefficient between individuals of the population was estimated to be 2.05?%??the highest individual coefficient was 10.31?%. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.  相似文献   

4.
This study aimed to describe the population genetic structure and evaluate the state of conservation of the genetic variability of Santa Inês sheep in Brazil. We used pedigree data of the Santa Inês breed available in electronic processing of the Brazilian Association of Sheep Breeders. A file with 20,206 records, which enabled the calculation of the genetic conservation index (GCI), individual inbreeding coefficient (F), change in inbreeding (ΔF), effective population size (Ne), effective number of founders (?e), effective number of ancestors (?ɑ), generation interval (L), average relatedness coefficient of each individual (AR), and Wright’s F-statistics (F IT, F IS, and F ST). For pedigree analysis and calculation of population parameters, the program ENDOG was used. The average inbreeding coefficient (\( \overline{F} \)) was 0.97% and the mean average relatedness (\( \overline{\mathrm{AR}} \)) 0.49%. The effective numbers of founders and ancestors were, respectively, 199 and 161. The average values of F and AR increased significantly over the years. The effective population size fluctuated over the years concurrently to oscillations in inbreeding rates, wherein N e reached just 68 in the year 2012. The mean average generation interval was 5.3 years. The Santa Inês breed in Brazil is under genetic drift process, with loss of genetic variation. It requires the implementation of a genetic management plan in the herd, for conservation and improvement of the breed.  相似文献   

5.
The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f e/f a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.  相似文献   

6.
A note on ENDOG: a computer program for analysing pedigree information   总被引：7，自引：0，他引：7  
  相似文献   

7.
Investigation of genetic structure on the basis of pedigree information requires indicators adapted to the specific context of the populations studied. On the basis of pedigree‐based estimates of diversity, we analysed genetic diversity, mating practices and gene flow among eight cat populations raised in France, five of them being single breeds and three consisting of breed groups with varieties that may interbreed. When computed on the basis of coancestry rate, effective population sizes ranged from 127 to 1406, while the contribution of founders from other breeds ranged from 0.7 to 16.4%. In the five breeds, FIS ranged between 0.96 and 1.83%, with this result being related to mating practices such as close inbreeding (on average 5% of individuals being inbred within two generations). Within the three groups of varieties studied, FIT ranged from 1.59 to 3%, while values were estimated between 0.04 and 0.91%, which was linked to various amounts of gene exchanges between subpopulations at the parental level. The results indicate that cat breeds constitute populations submitted to low selection intensity, contrasting with relatively high individual inbreeding level caused by close inbreeding practices.  相似文献   

8.
The objective of this research was to examine the population structure of full‐blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full‐blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST) and the effective population size (Ne) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full‐blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full‐blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.  相似文献   

9.
The Martina Franca (MF) donkey, an ancient native breed of Apulia, was mostly famous for mule production. The breed was at serious risk of extinction in the 1980s following the decrease in demand for draft animals because they were increasingly replaced by agricultural machinery. Much has been done in the last few decades to safeguard the existing donkey breeds, but the situation remains critical. Successful implementation of conservation measures includes an evaluation of the present degree of breed endangerment, so the aim of this work was to analyze the demographic and genetic parameters of this breed to suggest effective conservation strategies. With a current breed register counting less than 500 recorded animals, the pedigree data set included 1,658 MF donkeys born between 1929 and 2006. Analyses were carried out on the whole data set as well as on a smaller one consisting of 422 living animals. Demographic and genetic variability parameters were evaluated using the ENDOG (v4.6) software. The pedigree completeness level was evaluated as well as the generation length, which was calculated for each of the 4 gametic pathways. This information was obtained from animal birth date records together with those of their fathers and mothers. The effective number of founders (f(e)), the effective number of ancestors (f(a)), the founder genome (f(g)), individual inbreeding (F), average relatedness (AR), and the rate of inbreeding per generation were analyzed to describe the genetic variability of the population. Because pedigree depth and completeness were appropriate, especially regarding the current population, the parameters defining genetic variability, namely, f(e), f(a), f(g), F, and AR, could be reliably estimated. Analysis of these parameters highlighted the endangerment status of the MF donkey. Our special concern was with the increased percentage of males and females exhibiting increased AR values. Moreover, the effective size of the current population, 48.08, is slightly less than the range of the minimum effective size, and the rates of inbreeding per generation found in the current MF population exceed the maximum recommended level of 1%. Such a scenario heightens concerns over the endangered status of the MF breed and calls for proper conservation measures and breeding strategies, such as selecting individuals for mating when relationships are below 12.5%.  相似文献   

10.
The inbreeding coefficient (F) is used as a central parameter inferring a proportion of alleles identical by descent within an individual and by genetic variability within a population. The actual inbreeding coefficient varies around a central value, the inbreeding coefficient. C ockerham and W eir (1983) derived the method for computing the variance of inbreeding while reviewing several other methods. The variance of inbreeding in their report was considered to be of two components: one within population and the other between population of varied pedigrees. If pedigree is fixed, F is easily computed for an individual by the standard method (F alconer 1989). For domestic animals, pedigree information is usually available because it is requisite for a programme of genetic improvement. In this study, the variance of inbreeding coefficient was derived for an individual with a pedigree having a single path to a foundation animal.  相似文献   

11.
The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (Nge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on Nge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.  相似文献   

12.
Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (Ho) and expected (He) heterozygosity, individual coancestry coefficients (f and fm), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (fa), effective population size (Ne and Ne(m)) and founder genome equivalents (Ng and Ng(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (fm, Mk and Ng(m)). However, Ho and He showed the highest values for C1 and the molecular heterozygote deficiency within population (FIS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.  相似文献   

13.
The study investigates the genetic diversity present as well as its development in the Brown Cattle population of Switzerland from pedigree information. The population consisted of three subpopulations, the Braunvieh (BV), the original Braunvieh (OB) and the US‐Brown Swiss (BS). The BV is a cross of OB with BS where crossing still continues. The OB is without any genetic influence of BS. The diversity measures effective population size, effective number of ancestors (explaining 99% of reference genome) and founder genome equivalents were calculated for 11 reference populations of animals born in a single year from 1992 onwards. The BS‐subpopulation consisted of animals and their known ancestors which were used in the crossing scheme and was, therefore, quite small. The youngest animals were born in 2002, the oldest ones in the 1920s. Average inbreeding was by far the highest in BS, in spite of the lowest quality of pedigrees, and lowest in OB. Effective population size obtained from the difference between average inbreeding of offspring and their parents was, mostly due to the heavy use of few highly inbred BS‐sires, strongly overestimated in some BV‐reference populations. If this parameter was calculated from the yearly rate of inbreeding and a generation interval of 5 years, no bias was observed and ranking of populations from high to low was OB – BV – BS, i.e. equal to the other diversity parameters. The high genetic diversity found in OB was a consequence of the use of many natural service sires. Rate of decrease of effective number of ancestors was steeper in BV than OB was, however, equal for founder genome equivalents. Founder genome equivalents were more stable than effective population sizes calculated from the difference between average inbreeding of offspring and parents. The five most important ancestors contributed one‐third of the 2002‐reference genomes of BV and OB, in BV all were BS‐sires. The relative amount of BS‐genes in the BV‐genome increased from 59.2% to 78.5% during the 11 years considered.  相似文献   

14.
Franches‐Montagnes is the only native horse breed in Switzerland, therefore special efforts should be made for ensuring its survival. The objectives of this study were to characterize the structure of this population as well as genetic variability with pedigree data, conformation traits and molecular markers. Studies were focused to clarify if this population is composed of a heavy‐ and a light‐type subpopulation. Extended pedigree records of 3‐year‐old stallions (n = 68) and mares (n = 108) were available. Evaluations of body conformation traits as well as pedigree data and molecular markers did not support the two‐subpopulation hypothesis. The generation interval ranged from 7.8 to 9.3 years. The complete generation equivalent was high (>12). The number of effective ancestors varied between 18.9 and 20.1, whereof 50% of the genetic variability was attributed to seven of them. Genetic contribution of Warmblood horses ranged from 36% to 42% and that of Coldblood horses from 4% to 6%. The average inbreeding coefficient reached 6%. Inbreeding effective population size was 114.5 when the average increase of the inbreeding coefficient per year since 1910 was taken. Our results suggest that bottleneck situations occurred because of selection of a small number of sire lines. Promotion of planned matings between parents that are less related is recommended in order to avoid a reduction of the genetic diversity.  相似文献   

15.
Breeding circles allow genetic management in closed populations without pedigrees. In a breeding circle, breeding is split over sub‐populations. Each sub‐population receives breeding males from a single sub‐population and supplies breeding males to one other sub‐population. Donor‐recipient combinations of sub‐populations remain the same over time. Here, we derive inbreeding levels both mathematically and by computer simulation and compare them to actual inbreeding rates derived from DNA information in a real sheep population. In Veluws Heideschaap, a breeding circle has been in operation for over 30 years. Mathematically, starting with inbreeding levels and kinships set to zero, inbreeding rates per generation (ΔF) initially were 0.29%–0.47% within flocks but later converged to 0.18% in all flocks. When, more realistically, inbreeding levels at the start were high and kinship between flocks low, inbreeding levels immediately dropped to the kinship levels between flocks and rates more gradually converged to 0.18%. In computer simulations with overlapping generations, inbreeding levels and rates followed the same pattern, but converged to a lower ΔF of 0.12%. ΔF was determined in the real population with a 12 K SNP chip in recent generations. ΔF in the real population was 0.29%, based on markers to 0.41% per generation based on heterozygosity levels. This is two to three times the theoretically derived values. These increased rates in the real population are probably due to selection and/or the presence of dominant rams siring a disproportionate number of offspring. When these were simulated, ΔF agreed better: 0.35% for selection, 0.38% for dominant rams and 0.67% for both together. The realized inbreeding rates are a warning that in a real population inbreeding rates in a breeding circle can be higher than theoretically expected due to selection and dominant rams. Without a breeding circle, however, inbreeding rates would have been even higher.  相似文献   

16.
A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an effective population size of Ne = 30 animals in the recent cohort. Average generation interval was 3.07 years considering the whole pedigree, and in total, only 612 sows and boars generated offspring. Estimated heritabilities for both traits NBA and NW were 0.12, and the estimated genetic correlation between both traits was 0.96. The variance component due to the service sire was higher than in commercial pig breeds, presumably due to the widespread use of natural service boars. The EBVs for NBA from 333 selection candidates (63 boars and 270 sows) were used to determine optimal genetic contributions. Based on selected animals and their optimal genetic contributions, specific mating designs were evaluated to minimize inbreeding in the next generation. Best results were achieved when using a simulated annealing algorithm and allowing artificial insemination.  相似文献   

17.
The complete pedigree of two closed Iberian pig lines (Gamito and Torbiscal), with 798 and 4077 reproducers, has been used to measure the evolution of coancestry (f) and inbreeding (F) for autosomal and X‐linked genes along 16 and 28 respective equivalent discrete generations. At the last generation, the mean values of each line were f = 0.41 and 0.22, F = 0.35 and 0.18, fX = 0.46 and 0.22 and FX = 0.47 and 0.19, respectively. Other calculated parameters were the effective number of founders (final values, 6.8 and 35.2) and non‐founders (1.5 and 2.4), founder genome equivalents (1.2 and 2.3) and effective population size (16.0 and 57.7). Measures of Torbiscal effective size based on rates of coancestry (66.1), inbreeding (65.0) and linkage disequilibrium (71.0) were estimated from whole‐genome SNP genotyping data. Values of new and old inbreeding and their respective rates by generation were computed to detect purging effects of natural selection. The analysis of 6854 Torbiscal litters showed significant negative impacts of new and fast inbreeding on litter size, as expected from the purging hypothesis: ?0.20 born piglets per litter by a 10% of new inbreeding, and ?0.03 and ?0.02 piglets by 1% of total and new inbreeding rates, respectively. The analysis performed on 1274 litters of the Gamito line failed to show purging effects. The only significant results were reductions in ?0.91 and ?0.17 piglets by a 10% of old and X‐linked genes inbreeding, respectively. These results may be useful for some practical issues in conservation programs of farm or captive wild animals.  相似文献   

18.
The gene pool of the Japanese Black cattle has been completely closed to foreign breeds during the last 100 years. Genetic diversity of the Japanese Black cattle from 1960 to 2000 was monitored with three estimates of effective number of ancestors. Founder genome equivalent (Nge) accounts for all the causes of reduction of diversity. Effective number of founders (Nef) and non‐founders (Nenf) explain reduced diversity because of unequal genetic contributions of founders and random genetic drift in non‐founders, respectively. Further examination using gene dropping simulation was conducted to obtain information on survival of founder alleles. Unique founder alleles were dropped down along the actual pedigree with Monte Carlo procedure following Mendelian segregation rules, and generated genotypes of all the current live animals (612 959 heads). Pedigree records consisted of 2 075 188 animals was used for these analysis. The estimates of three effective numbers (Nef, Nge, and Nenf) decreased from 418.6 to 50.3, 86.6 to 7.3, and 109.2 to 8.5, respectively, during the period 1960–2000. The increasing differences between two kinds of genetic diversity indices derived from Nge and Nef showed that large part of the reduced diversity from 1980 was attributed to genetic drift caused by the intensive use of particular limited number of sires. In gene dropping analysis, probabilities of extinction of founder alleles were derived from their distributions of frequency in the current animals. Several founders showed low probabilities of allele extinction, irrespective of their relatively low genetic contributions. This suggests that these founders have lineages through which their alleles are surely transmitted to the current breed. The use of these founders as a strategy for recovering the genetic diversity was discussed.  相似文献   

19.
Abstract

To examine the genetic variation in two endangered Norwegian horse breeds, the pedigree structures were investigated, and key parameters such as inbreeding coefficients, effective population size, effective number of founders, effective number of ancestors and effective number of founder genomes were calculated. The data consisted of 31,142 individuals of the D?le horse and 1973 individuals of the Nordland/Lyngen horse, for which the complete generation equivalent was 10.5 and 7.2, respectively. In both breeds, the pedigree data were more than 98.5% complete in the fourth generation, allowing the rate of inbreeding and the effective population size to be precisely estimated, actually measuring the fractional loss of heterozygosity, comparable across generations (not so for the other measures). The level of inbreeding was about 12% in both breeds, with a rather wavy pattern during the past 50 years in the D?le. Considering the last generations only, the effective population size was found to be 152 in the D?le and 42 in the Nordland/Lyngen. For both populations selection in the future should be based on optimal contribution.  相似文献   

20.
旨在对广灵县优种驴场保种群体进行调查的基础上构建分子系谱,并对其种群的遗传结构进行分析。本研究采集保种群成年、体况良好的广灵驴（体重350~400 kg）颈静脉血10 mL（n=107）,其中公驴13份,母驴94份,抗凝处理后提取全血DNA。采用12个微卫星标记进行荧光PCR扩增后,用ABI3730测序仪进行分型。分型结果采用Cervus 2.0和Pedigraph 2.4软件构建分子系谱,同时采用STRUCTURE2.3和Fstat软件计算群体遗传参数,采用R语言的hclust函数绘制7头公驴及其后代的系统发生NJ树（邻接树）。结果,对107头种驴进行了分子系谱构建,找到了30头子代的父亲和7头子代的母亲,系谱可靠性>90%;微卫星标记的平均观测杂合度（HObs）和多态信息含量（PIC）分别为0.676 5和0.593 9,标记遗传多样性较高;NJ树对7个公驴家系进行了聚类;群体分化系数（FST）为0.184,群体平均近交系数（FIT）为0.033,群体内近交系数（FIS）为-0.238,且群体处于哈代-温伯格平衡状态,存在很弱的近交。本研究建立了广灵驴保种群可靠性较高的分子系谱并对其遗传结构进行了分析,证明该群体遗传多态性较高,群体近交系数较低,处于较好的保种状态,具有较大的品种资源开发潜力。  相似文献   

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